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Abstract: We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness... (Update)
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0.7: Estimating seed sensitivity on homogeneous alignments - Kucherov, Noé, Ponty (2003) (Correct)
0.5: Multi-Seed Lossless Filtration (Extended Abstract) - Kucherov, Noe, Roytberg (2004) (Correct)
0.5: YASS: enhancing the sensitivity of DNA similarity search - Noe, Kucherov (2005) (Correct)
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BibTeX entry: (Update)
KUCHEROV, G., NOE, L., AND PONTY, Y. Estimating seed sensitivity on homogeneous alignments. In Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering (BIBE http://citeseer.ist.psu.edu/742939.html More
@misc{ kucherov-estimating,
author = "G. KUCHEROV and L. NOE and Y. PONTY",
title = "Estimating seed sensitivity on homogeneous alignments",
text = "KUCHEROV, G., NOE, L., AND PONTY, Y. Estimating seed sensitivity on homogeneous
alignments. In Proceedings of the IEEE 4th Symposium on Bioinformatics and
Bioengineering (BIBE",
url = "citeseer.ist.psu.edu/742939.html" }
Citations (may not include all citations):431 Basic Local Alignment Search Tool (context) - Altschul, Gish et al. - 1990
266 Gapped BLAST and PSI-BLAST: a new generation of protein data.. - Altschul, Madden et al. - 1997
240 Identification of common molecular subsequences - Smith, Waterman - 1981
155 Improved tools for biological sequence comparison (context) - Lipman, Pearson - 1988
36 Flash: A fast look-up algorithm for string homology (context) - Califano, Rigoutsos - 1993
33 PatternHunter: Faster and more sensitive homology search - Ma, Tromp et al. - 2002
25 Applications and statistics for multiple high-scoring segmen.. (context) - Karlin, Altschul - 1993
23 BLAT--the BLAST-like alignment tool (context) - Kent - 2002
18 Uniform random generation of strings in a context-free langu.. (context) - Hickey, Cohen - 1983
17 Designing seeds for similarity search in genomic DNA (context) - Buhler, Keich et al. - 2003
15 Multiple filtration and approximate pattern matching (context) - Pevzner, Waterman - 1995
14 Human--mouse alignments with BLASTZ (context) - Schwartz, Kent et al. - 2003
12 Better filtering with gapped q-grams - Burkhardt, Karkkainen - 2003
11 Vector seeds: an extension to spaced seeds allows substantia.. - Brejova, Brown et al. - 2003
9 Optimal spaced seeds for Hidden Markov Models (context) - Brejova, Brown et al. - 2003
8 and selection algorithms for combinatorial objects (context) - Wilf, setting et al. - 1977
6 Efficient large-scale sequence comparison by locality-sensit.. (context) - Buhler - 2001
6 YASS: Similarity search in DNA sequences - Noe, Kucherov - 2003
6 A linear time algorithm for finding all maximal scoring subs.. - Ruzzo, Tompa - 1999
5 Good spaced seeds for homology search (context) - Choi, Zeng et al. - 2003
3 Chance and significance in protein and DNA sequence analysis (context) - Karlin, Brendel - 1992
3 Sensitivity analysis and efficient method for identifying op.. (context) - Choi, Zhang - 2003
2 to appear in Discrete Applied Mathematics (context) - Keich, Li et al. - 2002
1 Generation aleatoire et uniforme de mots de langages rationn.. (context) - Denise - 1996
The graph only includes citing articles where the year of publication is known.
Documents on the same site (http://www.lifl.fr/~noe/publications.html): More
YASS: enhancing the sensitivity of DNA similarity search - Noe, Kucherov (2005) (Correct)
Multi-Seed Lossless Filtration (Extended Abstract) - Kucherov, Noe, Roytberg (2004) (Correct)
Unknown - Apport De Recherche (Correct)
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